[gmx-users] High temperature Simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 17 13:33:58 CEST 2011

bipin singh wrote:
> As far as I know we do energy minimization at room temperature only.

Energy minimization is (theoretically) at 0 K, as there are no velocities and it 
is not a true dynamical process.

> Only during equilibration
> (NVT and NPT) we use high temperature for maintaining proper density
> before starting the final production run.

Maintaining density is but one possible goal for NPT; defining the desired 
ensemble and therefore the sampling distribution is the main reason.


> On Mon, Oct 17, 2011 at 15:15, Kavyashree M <hmkvsri at gmail.com> wrote:
>> Dear users,
>> For simulating a protein at high temperature (more than 300K,
>> less than 400K) using OPLSAA forcefield, what are the parameters
>> other than Temperature that need to be taken care of?
>> Does the energy minimization step also needs to be done at high
>> temperature? (here my aim is not to simulate an unfolding event)
>> I have a reference -
>> Biophysical Journal Volume 94 June 2008 4444–4453
>> Any other references or suggestions will be helpful.
>> Thanking you
>> With Regards
>> M. Kavyashree
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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